And I'm Renee Montagne. The largest U.S. prison in Afghanistan - containing over 3,000 inmates - was handed over to Afghan control this morning. But the transfer was not without controversy. Several dozen prisoners, including some foreign terrorist suspects, were kept in American custody.

The prison at Bagram Air Base, north of Kabul, has been a sore point in U.S.-Afghan relations for years. To many Afghans, it's viewed as a Guantanamo in their midst. Six months ago, the Afghan and U.S. governments struck a deal to transfer control of the prison to Afghan security forces. But at the last minute, the U.S. balked at transferring those few last prisoners.

To find out more, we go to NPR's Soraya Sarhaddi Nelson, who's in Kabul. Good morning.

SORAYA SARHADDI NELSON, BYLINE: Good morning, Renee.

MONTAGNE: So tell us a little more about this prison, and why it is that the Afghan government demanded that it be handed over now instead of after U.S. forces leave the country, in 2014.

NELSON: Well, it's formerly known as the Parwan Detention Facility, and it's just on the edge, or on the cusp, of Bagram Air Base, which is north of Kabul. As you mentioned, it's been compared to Guantanamo. It's also been compared to Abu Ghraib in Iraq. Basically, key Taliban prisoners and terrorism suspects are held at this facility. Most of them are Afghan nationals.

But the facility has had a lot of controversy. It's known for its lengthy detentions of Afghans, who are brought here without due process. There have also been reports over the years of detainees being mistreated and tortured, including two deaths of prisoners in Bagram, in 2002. So it's pretty obvious to see why Afghans view this prison as a symbol of American domination of their country.

And while President Karzai embraces the need for Western troops here, he really wants this facility under Afghan control. He's made the future presence of foreign troops in Afghanistan contingent on that transfer,. And that led to the memorandum of understanding, which was signed by both sides six months ago, for that transfer to take place yesterday.

MONTAGNE: What was it about these several dozen prisoners, that caused the U.S. to delay their transfer in this larger transfer?

NELSON: Well, no one will say exactly what the problem was, at least on the American side. But there certainly is concern about the Afghan follow-through on the agreement that was signed in March by Defense Minister Wardak. He was ousted last month by the Afghan Parliament, and there's some concerns, again, that - some statements, apparently, that came up, that made the Americans somewhat concerned that perhaps this agreement was not going to be followed to the letter by the Afghan side.

It's important to note that the memorandum of understanding includes a provision that the Afghans consult with the U.S. about any planned release of detainees.

MONTAGNE: So what, then, is the Afghan government doing now, in response to the delay of these few prisoners - even though the larger transfer is taking place?

NELSON: Well, there are a couple of things happening. One is a lavish ceremony that took place today in the Bagram area, where the Afghans took control over the detention facility. But notably absent from the ceremony were the coalition commander, General John Allen, and the U.S. ambassador, James Cunningham. They last were in President Karzai's office on Saturday, in what the Afghan media described as a tense meeting. And this is something that the U.S. officials dispute.

But nevertheless, President Karzai, after this meeting, fired off a terse statement that more or less, said that the transfer better happen, or his country would view it as a serious breach of Afghan sovereignty. U.S. officials say that they won't proceed with the transfer of any more prisoners unless they are assured that the memorandum of understanding is being followed to the letter. And it's important to note, also, at the ceremony that an Afghan general said 12 detainees were being released after they reviewed their files. And so they were at the ceremony, and they were going to be released later today.